After gazium raiders use a Planeteer squadron's secret code to lure them away from a gazium theft, all members of that squad, including Capt. Tommy Tomorrow and Capt. Lon Vurian, are placed under investigation. Evidence points to Tomorrow, who is brought before General Nordyke at Supreme Headquarters on Earth. In reality, it is all part of a plan by Nordyke and Tomorrow to uncover the real Planeteer traitor. Tomorrow is found guilty and sentenced to 5 years in Planeteer Prison. Hours later, he escapes. On Uranus, Dr. Klik watches the news of the "renegade Planeteer" with great interest.

Using the stolen gazium, Dr. Klik succeeds in greatly expanding the size of a single atom. This strange atom is inhabited by fantastic creatures which, when expanded to scale, will be indestructible. Klik sends his gang to find Tommy Tomorrow. They soon locate him in a shady Venusian cafe, and Tomorrow is brought to Kilk's laboratory on Uranus. Klik explains that he will destroy one of the planets and replace it with his atom world. Tomorrow makes his way back to Earth to speak with General Nordyke, but Nordyke is in a coma and the Acting Commandant knows nothing of their secret plan.

With Vurian's help, Tomorrow escapes capture and returns to Klik's hideout. Tomorrow tells Klik that he wants to be his partner, and asks to know more about the atom-planet. Suddenly, Vurian arrives and blows Tomorrow's cover. Klik's freezes the two heroes, then leaves to implement his plan to destroy Mars and replace it with his atom-world. Tomorrow is able to free himself, and fires a beam from Klik's machine that starts to reverse the atom's expansion. While Tomorrow frees Vurian, the Planeteers capture Klik. Tomorrow is cleared by Gen. Nordyke, who has finally awoken from his coma.